GeneSPIDER statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GeneSPIDER

Tool usage distribution map

This map represents all the scientific publications referring to GeneSPIDER per scientific context
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Associated diseases


Popular tool citations

chevron_left Gene regulatory network inference chevron_right
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GeneSPIDER specifications


Unique identifier OMICS_31758
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.11
Stability Stable
git, Glmnet, JSONlab, xml4mat, CVX, aracne
Maintained Yes


No version available



  • person_outline Erik Sonnhammer

Publications for GeneSPIDER

GeneSPIDER citations


Functional association networks as priors for gene regulatory network inference

PMCID: 4058914
PMID: 24931976
DOI: 10.1093/bioinformatics/btu285

[…] rated synthetic networks and datasets for three of the DREAM competitions and this program uses nonlinear dynamical models of transcription and translation. Another synthetic data generation program, GeneSpider (Tjärnberg et al., 2014, manuscript in preparation), uses a linear dynamical model of transcription. These two programs were used in our study to generate synthetic data.Prior knowledge may […]


Downstream genes of Pax6 revealed by comprehensive transcriptome profiling in the developing rat hindbrain

BMC Dev Biol
PMCID: 2818624
PMID: 20082710
DOI: 10.1186/1471-213X-10-6
call_split See protocol

[…] les, with color density indicating reliability. Because the GeneChip RAE 230 gene titles that were provided by Affymetrix were sometimes incorrect, the master gene table for RAE 230 was updated using GeneSpider, which automatically submitted each gene to three databases: Entrez Gene, GenBank and UniGene. If required, gene annotation was manually submitted to multiple databases including UCSC Genom […]

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GeneSPIDER institution(s)
Stockholm Bioinformatics Center, Stockholm University, Sweden; Science for Life Laboratory, Stockholm University, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Sweden; Department of Physics, Chemistry and Biology/Bioinformatics, Linköping University, Sweden; Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan

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